Limits...
A transcriptional time-course analysis of oral vs. aboral whole-body regeneration in the Sea anemone Nematostella vectensis

View Article: PubMed Central - PubMed

ABSTRACT

Background: The ability of regeneration is essential for the homeostasis of all animals as it allows the repair and renewal of tissues and body parts upon normal turnover or injury. The extent of this ability varies greatly in different animals with the sea anemone Nematostella vectensis, a basal cnidarian model animal, displaying remarkable whole-body regeneration competence.

Results: In order to study this process in Nematostella we performed an RNA-Seq screen wherein we analyzed and compared the transcriptional response to bisection in the wound-proximal body parts undergoing oral (head) or aboral (tail) regeneration at several time points up to the initial restoration of the basic body shape. The transcriptional profiles of regeneration responsive genes were analyzed so as to define the temporal pattern of differential gene expression associated with the tissue-specific oral and aboral regeneration. The identified genes were characterized according to their GO (gene ontology) assignations revealing groups that were enriched in the regeneration process with particular attention to their affiliation to the major developmental signaling pathways. While some of the genes and gene groups thus analyzed were previously known to be active in regeneration, we have also revealed novel and surprising candidate genes such as cilia-associated genes that likely participate in this important developmental program.

Conclusions: This work highlighted the main groups of genes which showed polarization upon regeneration, notably the proteinases, multiple transcription factors and the Wnt pathway genes that were highly represented, all displaying an intricate temporal balance between the two sides. In addition, the evolutionary comparison performed between regeneration in different animal model systems may reveal the basic mechanisms playing a role in this fascinating process.

Electronic supplementary material: The online version of this article (doi:10.1186/s12864-016-3027-1) contains supplementary material, which is available to authorized users.

No MeSH data available.


A general analysis and comparison of side and time course expression trends. a. Distribution of genes in either the oral or physal regenerating sides according to their time course response pattern: always upregulated, always downregulated or other, having a more complex trend. Genes were considered always up or downregulated if all time points of regeneration were at least 1.6 fold higher or lower than hour 0, respectively. b. Distribution of genes being either always upregulated or downregulated according to their oral or physal response in regeneration. c. The number of oral or physal genes being up or downregulated at each time point along regeneration. Genes were considered up or downregulated at each time point if their expression was at least 1.6 fold different compared to their expression level in the previous time point d. Examples of qPCR results of highly DE genes that show a similar expression pattern in both sides during early regeneration and a prominent divergence during later regeneration
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC5015328&req=5

Fig3: A general analysis and comparison of side and time course expression trends. a. Distribution of genes in either the oral or physal regenerating sides according to their time course response pattern: always upregulated, always downregulated or other, having a more complex trend. Genes were considered always up or downregulated if all time points of regeneration were at least 1.6 fold higher or lower than hour 0, respectively. b. Distribution of genes being either always upregulated or downregulated according to their oral or physal response in regeneration. c. The number of oral or physal genes being up or downregulated at each time point along regeneration. Genes were considered up or downregulated at each time point if their expression was at least 1.6 fold different compared to their expression level in the previous time point d. Examples of qPCR results of highly DE genes that show a similar expression pattern in both sides during early regeneration and a prominent divergence during later regeneration

Mentions: Further analysis of the general time course trends revealed that about half of the DE genes could be defined as being always up or down-regulated throughout the sampled time points of regeneration, while the remaining genes displayed more complex expression patterns, with one or more changes in the direction of expression along the time course (Fig. 3a). We characterized a gene as being always upregulated if all time points of regeneration showed an expression level higher than that of hour 0, and always downregulated if expression in all time points were lower than in hour 0. When examining the expression modes in the overall always up and downregulated genes, the largest group consisted of genes that behaved similarly in both sides (~50 %), while the rest were either oral or physal specific (Fig. 3b). Of the genes that are regulated in one side, the oral side contained more of these and this was particularly evident among the downregulated genes. A list of the genes and their trend of expression can be found in Additional file 3: Table S2.Fig. 3


A transcriptional time-course analysis of oral vs. aboral whole-body regeneration in the Sea anemone Nematostella vectensis
A general analysis and comparison of side and time course expression trends. a. Distribution of genes in either the oral or physal regenerating sides according to their time course response pattern: always upregulated, always downregulated or other, having a more complex trend. Genes were considered always up or downregulated if all time points of regeneration were at least 1.6 fold higher or lower than hour 0, respectively. b. Distribution of genes being either always upregulated or downregulated according to their oral or physal response in regeneration. c. The number of oral or physal genes being up or downregulated at each time point along regeneration. Genes were considered up or downregulated at each time point if their expression was at least 1.6 fold different compared to their expression level in the previous time point d. Examples of qPCR results of highly DE genes that show a similar expression pattern in both sides during early regeneration and a prominent divergence during later regeneration
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC5015328&req=5

Fig3: A general analysis and comparison of side and time course expression trends. a. Distribution of genes in either the oral or physal regenerating sides according to their time course response pattern: always upregulated, always downregulated or other, having a more complex trend. Genes were considered always up or downregulated if all time points of regeneration were at least 1.6 fold higher or lower than hour 0, respectively. b. Distribution of genes being either always upregulated or downregulated according to their oral or physal response in regeneration. c. The number of oral or physal genes being up or downregulated at each time point along regeneration. Genes were considered up or downregulated at each time point if their expression was at least 1.6 fold different compared to their expression level in the previous time point d. Examples of qPCR results of highly DE genes that show a similar expression pattern in both sides during early regeneration and a prominent divergence during later regeneration
Mentions: Further analysis of the general time course trends revealed that about half of the DE genes could be defined as being always up or down-regulated throughout the sampled time points of regeneration, while the remaining genes displayed more complex expression patterns, with one or more changes in the direction of expression along the time course (Fig. 3a). We characterized a gene as being always upregulated if all time points of regeneration showed an expression level higher than that of hour 0, and always downregulated if expression in all time points were lower than in hour 0. When examining the expression modes in the overall always up and downregulated genes, the largest group consisted of genes that behaved similarly in both sides (~50 %), while the rest were either oral or physal specific (Fig. 3b). Of the genes that are regulated in one side, the oral side contained more of these and this was particularly evident among the downregulated genes. A list of the genes and their trend of expression can be found in Additional file 3: Table S2.Fig. 3

View Article: PubMed Central - PubMed

ABSTRACT

Background: The ability of regeneration is essential for the homeostasis of all animals as it allows the repair and renewal of tissues and body parts upon normal turnover or injury. The extent of this ability varies greatly in different animals with the sea anemone Nematostella vectensis, a basal cnidarian model animal, displaying remarkable whole-body regeneration competence.

Results: In order to study this process in Nematostella we performed an RNA-Seq screen wherein we analyzed and compared the transcriptional response to bisection in the wound-proximal body parts undergoing oral (head) or aboral (tail) regeneration at several time points up to the initial restoration of the basic body shape. The transcriptional profiles of regeneration responsive genes were analyzed so as to define the temporal pattern of differential gene expression associated with the tissue-specific oral and aboral regeneration. The identified genes were characterized according to their GO (gene ontology) assignations revealing groups that were enriched in the regeneration process with particular attention to their affiliation to the major developmental signaling pathways. While some of the genes and gene groups thus analyzed were previously known to be active in regeneration, we have also revealed novel and surprising candidate genes such as cilia-associated genes that likely participate in this important developmental program.

Conclusions: This work highlighted the main groups of genes which showed polarization upon regeneration, notably the proteinases, multiple transcription factors and the Wnt pathway genes that were highly represented, all displaying an intricate temporal balance between the two sides. In addition, the evolutionary comparison performed between regeneration in different animal model systems may reveal the basic mechanisms playing a role in this fascinating process.

Electronic supplementary material: The online version of this article (doi:10.1186/s12864-016-3027-1) contains supplementary material, which is available to authorized users.

No MeSH data available.